Nanoscale control of matter has led to enormous advances in many fields. In the biological and medical fields continued advances will allow for an unprecedented ability to examine and manipulate biological molecules and reactions. To achieve this, efficient methods for trapping, identifying, and sensing properties of biomolecules are needed.
One biomedical application in particular, genome sequencing, is a prime example of an application amenable to such a nanoscale approach. Current methods of genome sequencing such as chain-termination gel electrophoresis are slow and costly. This, coupled with the fact that a human genome contains approximately 3 billion base pairs makes sequencing even a single human genome a monumental task.
The possibility of direct genome sequencing using electronic measurements, wherein each base pair is identified as it basses by a nanoscale sensor, is potentially orders of magnitude faster and proportionally less costly then existing methods. These new techniques could enable sequencing of any individual's genome to prevent, diagnose, and treat diseases, potentially leading to a new genome-based medical practice.
One method of directly sequencing DNA involves translocating a fragment of Single-Stranded DNA (ssDNA) through a nanogap or a nanopore. These nanopores confine the DNA and allow for measurement of its properties as it translocates through the nanopore. Differences in the structure of the different nucleotides give rise to measurable effects which can be detected. Several measurements can distinguish between different bases, allowing for sequencing the DNA as it passes through the nanopore. If an ionic current is flowing through a nanopore, it has been found that DNA translocating through the pore masks the ionic current in a way specific to the nucleotide instantaneously passing through the pore. Alternatively, a bias applied across the transverse direction of the nucleotide can measure the capacitance or conductance of that specific nucleotide.
Repeatable measurements of the base specific signature of each nucleotide depends critically on its relative geometry during translocation. For example, it has been found that the variation in the transverse conductance due to the geometry of a base relative to an electrode can easily outweigh the differences between different types of nucleotides. Differences in the orientation and position of nucleotides relative to sensors must be minimized to make such a system feasible. Because an ssDNA is only about a nanometer wide, trapping methods that can achieve control on this scale are required. Further, DNA sequencing occurs in an aqueous or electrolytic environment, and an appropriate method of trapping the DNA must be compatible in such conditions. In a broader context, however, the general techniques of trapping and manipulating particles in liquid environment at a nanoscale resolution are important for a number of applications beyond DNA sequencing. Specifically, many molecules of interest become charged upon dissociation in an aqueous environment, and such a method could enable efficient trapping, sensing, identifying and sorting of these molecules.
Over the last few decades, a variety of manipulation techniques have been developed to achieve trapping of particles in liquids. These methods include optical tweezers, acoustic tweezers, and magnetic tweezers. These methods, however, can require complicated setups that have a low potential for integration into compact and cost effective devices. Because of this, increasing use has been made of electrical forces for achieving manipulations of particles in liquids.
Dielectrophoresis (DEP) forces arise from an object's polarizability. By applying a nonuniform electric field, it is possible to induce a dipole moment on an uncharged particle and create either an attractive or repulsive force. Using DEP it is possible to trap small particles in solutions. Indeed, the electrical trapping of objects in solution has so far been done primarily by DEP. DEP forces, however, are relatively weak, especially for smaller targets since the forces scale with the volume of the trapped object. Particles with diameters below 1 μm, for example, cannot be trapped by DEP as Brownian motion overwhelms the DEP forces. For this reason DEP based traps are not attractive for detection of very small biomolecules, such as ssDNA bases for direct sequencing.
Electrophoresis, in contrast, makes use of the interaction of an object's fixed charge and an electric field. Electrophoresis depends upon the amount of charge rather than polarizability, and is a first order interaction with the electrical field. While useful for moving particles, the multipole fields are unsuitable for trapping applications. This is because a charged particle cannot be stably held in a multipole electrostatic field due to the saddle shape of the potential that results from Laplace's equation. While a charged particle may be confined in one dimension, it will necessarily be unconfined in another. Although this would seem to preclude electrophoretic traps, one can get around this problem by using a time-varying field.
One such system is the anti-Brownian electrophoretic trap (ABEL) based on a feed-back mechanism. In this system the computer visually tracks the trajectory of a charged particle. Using this information, the computer calculates a feedback voltage which is applied to electrodes arranged around a trapping volume containing the target particle. The applied feedback voltage creates an force to counteract the particles motion and return it to the center of the trapping volume. This technique requires a visible target and stability depends upon a fast sampling rate. These limitations make the technique unsuitable for many applications.
There remains a need in the art for systems and methods for controlling charged particles in liquids. Preferably such a system would utilize the strong electrophoresis force without requiring complicated setups or detection schemes. Such a system is desirable as it could enable efficient control of biomolecules for a variety of applications including DNA sequencing.
In contrast to trapping techniques in a liquid environment, trapping charged particles in vacuum and gaseous environments using electromagnetism is a mature field. It is known that atomic ions and other charged particles can be confined by particular arrangements of electromagnetic fields in these environments. One such device is a Paul trap, which can be used to dynamically confine particles in vacuum or gas through spatially inhomogeneous and alternating radio frequency (RF) electrical fields. In this type of device a set of electrodes generates an alternating quadrupole potential which can provide confinement in two or three dimensions. While at any given moment the potential within the trap is an unstable saddle point, changing the orientation of this saddle point rapidly by providing an appropriate RF field can in fact create a dynamically stable trap.
Paul traps are used in vacuum and gaseous environments today for a number of applications including analytical chemistry and aerosol research, and their version, a linear Paul trap, is an important component of Mass Spectrometry instruments. While Paul traps exhibit many properties which are attractive as a potential trapping method for charged particles in liquids, it has been the general consensus that such a device was incompatible with a liquid environment. Polarization of the liquid, thermal fluctuations due to Brownian motion, charge screening, and viscosity were all effects indicated that such a device was impossible. To date, no Paul traps have been demonstrated in a liquid environment.
Accordingly, presently there is a need in the art for Paul traps capable of trapping charged particles in liquids. Additionally, there is a need for incorporating these novel Paul traps into systems for controlling, sensing, and identifying charged particles in a liquid environment.